protegeproject / protege

Protege Desktop
http://protege.stanford.edu
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Render by Prefixed Annotation Property displays two consecutive prefixes #327

Closed wismill closed 8 years ago

wismill commented 8 years ago

Hi, the entity renderer displays two consecutive prefixes for the classes: "owl:owl:Thing", "skos:skos:Concept".

This happens when using the option "Render by prefixed annotation property" of the entity rendering. By the way, the classes are always displayed prefixed but not the individuals, regardless to the option chosen.

I am using the latest development version of Protégé.

csnyulas commented 8 years ago

This is very unusual. We have never have such thing reported. Could you send us a screen shot? Here is a few additional questions to try to debug it:

matthewhorridge commented 8 years ago

I know what has caused this. A fix should be in beta-23.

wismill commented 8 years ago

Prefixes:

@prefix :        <http://example.org/ontologies/mathematics/lattice%20theory/0.1/> .
@prefix math:    <http://example.org/ontologies/mathematics/0.1/> .
@prefix rel:     <http://example.org/ontologies/mathematics/relations/0.1/> .
@prefix set:     <http://example.org/ontologies/mathematics/set%20theory/0.1/> .
@prefix algebra: <http://example.org/ontologies/mathematics/universal%20algebra/0.1/> .
@prefix graph:   <http://example.org/ontologies/mathematics/graph%20theory/0.1/> .
@prefix cat:     <http://example.org/ontologies/mathematics/category%20theory/0.1/> .
@prefix order:   <http://example.org/ontologies/mathematics/order%20theory/0.1/> .

@prefix skos:  <http://www.w3.org/2004/02/skos/core#> .
@prefix skoxl: <http://www.w3.org/2008/05/skos-xl#> .
@prefix rdf:   <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix rdfs:  <http://www.w3.org/2000/01/rdf-schema#> .
@prefix owl:   <http://www.w3.org/2002/07/owl#> .
@prefix dct:   <http://purl.org/dc/terms/> .

Log:


C:\repositories\protege\protege-desktop\target\protege-5.0.0-beta-23-SNAPSHOT-platform-independent\Protege-5.0.0-beta-23-SNAPSHOT>setlocal

C:\repositories\protege\protege-desktop\target\protege-5.0.0-beta-23-SNAPSHOT-platform-independent\Protege-5.0.0-beta-23-SNAPSHOT>cd /d C:\repositories\protege\protege-desktop\target\protege-5.0.0-beta-23-SNAPSHOT-platform-independent\Protege-5.0.0-beta-23-SNAPSHOT\ 

C:\repositories\protege\protege-desktop\target\protege-5.0.0-beta-23-SNAPSHOT-platform-independent\Protege-5.0.0-beta-23-SNAPSHOT>java -Xmx500M -Xms200M -XX:CompileCommand=exclude,javax/swing/text/GlyphView,getBreakSpot -DentityExpansionLimit=100000000 -Dlogback.configurationFile=conf/logback.xml -Dfile.encoding=utf-8 -Dorg.protege.plugin.dir=plugins -classpath bundles/guava.jar;bundles/jansi.jar;bundles/logback-classic.jar;bundles/logback-core.jar;bundles/slf4j-api.jar;bin/org.apache.felix.main.jar;bin/protege-launcher.jar org.protege.osgi.framework.Launcher  
CompilerOracle: exclude javax/swing/text/GlyphView.getBreakSpot
17:11:05,905 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [conf/logback.xml] at [file:/C:/repositories/protege/protege-desktop/target/protege-5.0.0-beta-23-SNAPSHOT-platform-independent/Protege-5.0.0-beta-23-SNAPSHOT/conf/logback.xml]
17:11:05,959 |-INFO in ch.qos.logback.classic.joran.action.ConfigurationAction - debug attribute not set
17:11:05,965 |-INFO in ch.qos.logback.classic.joran.action.ConfigurationAction - Setting ReconfigureOnChangeFilter scanning period to 10 seconds
17:11:05,965 |-INFO in ReconfigureOnChangeFilter{invocationCounter=0} - Will scan for changes in [[C:\repositories\protege\protege-desktop\target\protege-5.0.0-beta-23-SNAPSHOT-platform-independent\Protege-5.0.0-beta-23-SNAPSHOT\conf\logback.xml]] every 10 seconds. 
17:11:05,965 |-INFO in ch.qos.logback.classic.joran.action.ConfigurationAction - Adding ReconfigureOnChangeFilter as a turbo filter
17:11:05,974 |-INFO in ch.qos.logback.core.joran.action.AppenderAction - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
17:11:05,977 |-INFO in ch.qos.logback.core.joran.action.AppenderAction - Naming appender as [stdout]
17:11:06,016 |-INFO in ch.qos.logback.core.ConsoleAppender[stdout] - Enabling JANSI WindowsAnsiOutputStream for the console.
17:11:06,140 |-WARN in ch.qos.logback.core.ConsoleAppender[stdout] - Failed to create WindowsAnsiOutputStream. Falling back on the default stream. ch.qos.logback.core.util.DynamicClassLoadingException: Failed to instantiate type org.fusesource.jansi.WindowsAnsiOutputStream
    at ch.qos.logback.core.util.DynamicClassLoadingException: Failed to instantiate type org.fusesource.jansi.WindowsAnsiOutputStream
    at  at ch.qos.logback.core.util.OptionHelper.instantiateByClassNameAndParameter(OptionHelper.java:73)
    at  at ch.qos.logback.core.util.OptionHelper.instantiateByClassNameAndParameter(OptionHelper.java:42)
    at  at ch.qos.logback.core.ConsoleAppender.getTargetStreamForWindows(ConsoleAppender.java:94)
    at  at ch.qos.logback.core.ConsoleAppender.start(ConsoleAppender.java:85)
    at  at ch.qos.logback.core.joran.action.AppenderAction.end(AppenderAction.java:96)
    at  at ch.qos.logback.core.joran.spi.Interpreter.callEndAction(Interpreter.java:317)
    at  at ch.qos.logback.core.joran.spi.Interpreter.endElement(Interpreter.java:196)
    at  at ch.qos.logback.core.joran.spi.Interpreter.endElement(Interpreter.java:182)
    at  at ch.qos.logback.core.joran.spi.EventPlayer.play(EventPlayer.java:62)
    at  at ch.qos.logback.core.joran.GenericConfigurator.doConfigure(GenericConfigurator.java:149)
    at  at ch.qos.logback.core.joran.GenericConfigurator.doConfigure(GenericConfigurator.java:135)
    at  at ch.qos.logback.core.joran.GenericConfigurator.doConfigure(GenericConfigurator.java:99)
    at  at ch.qos.logback.core.joran.GenericConfigurator.doConfigure(GenericConfigurator.java:49)
    at  at ch.qos.logback.classic.util.ContextInitializer.configureByResource(ContextInitializer.java:77)
    at  at ch.qos.logback.classic.util.ContextInitializer.autoConfig(ContextInitializer.java:152)
    at  at org.slf4j.impl.StaticLoggerBinder.init(StaticLoggerBinder.java:85)
    at  at org.slf4j.impl.StaticLoggerBinder.<clinit>(StaticLoggerBinder.java:55)
    at  at org.slf4j.LoggerFactory.bind(LoggerFactory.java:141)
    at  at org.slf4j.LoggerFactory.performInitialization(LoggerFactory.java:120)
    at  at org.slf4j.LoggerFactory.getILoggerFactory(LoggerFactory.java:331)
    at  at org.slf4j.LoggerFactory.getLogger(LoggerFactory.java:283)
    at  at org.protege.osgi.framework.Launcher.<init>(Launcher.java:33)
    at  at org.protege.osgi.framework.Launcher.main(Launcher.java:242)
Caused by: java.lang.reflect.InvocationTargetException
    at  at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
    at  at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source)
    at  at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Source)
    at  at java.lang.reflect.Constructor.newInstance(Unknown Source)
    at  at ch.qos.logback.core.util.OptionHelper.instantiateByClassNameAndParameter(OptionHelper.java:68)
    at  ... 22 common frames omitted
Caused by: java.io.IOException: Could not get the screen info: D e r   V o r g a n g   w u r d e   e r f o l g r e i c h   b e e n d e t . 

    at  at org.fusesource.jansi.WindowsAnsiOutputStream.getConsoleInfo(WindowsAnsiOutputStream.java:104)
    at  at org.fusesource.jansi.WindowsAnsiOutputStream.<init>(WindowsAnsiOutputStream.java:97)
    at  ... 27 common frames omitted
17:11:06,141 |-INFO in ch.qos.logback.core.joran.action.AppenderAction - About to instantiate appender of type [ch.qos.logback.core.FileAppender]
17:11:06,142 |-INFO in ch.qos.logback.core.joran.action.AppenderAction - Naming appender as [files]
17:11:06,168 |-INFO in ch.qos.logback.core.FileAppender[files] - File property is set to [C:\Users\user123/.protege/logs/protege.log]
17:11:06,170 |-INFO in ch.qos.logback.classic.joran.action.RootLoggerAction - Setting level of ROOT logger to INFO
17:11:06,170 |-INFO in ch.qos.logback.core.joran.action.AppenderRefAction - Attaching appender named [stdout] to Logger[ROOT]
17:11:06,170 |-INFO in ch.qos.logback.core.joran.action.AppenderRefAction - Attaching appender named [files] to Logger[ROOT]
17:11:06,170 |-INFO in ch.qos.logback.classic.joran.action.ConfigurationAction - End of configuration.
17:11:06,171 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@3ecf72fd - Registering current configuration as safe fallback point

******************************************************************************** 
**                                  Protege                                   ** 
******************************************************************************** 
 
----------------- Initialising and Starting the OSGi Framework ----------------- 
FrameworkFactory Class: org.apache.felix.framework.FrameworkFactory 
 
The OSGi framework has been initialised 
------------------------------- Starting Bundles ------------------------------- 
Starting bundle org.protege.common 
Starting bundle org.eclipse.equinox.common 
Starting bundle org.eclipse.equinox.supplement 
Starting bundle org.eclipse.equinox.registry 
Starting bundle org.protege.editor.core.application 
Starting bundle org.apache.commons.io 
Starting bundle com.google.guava 
Not starting bundle com.google.inject.assistedinject explicitly because it is a fragment bundle. 
Not starting bundle com.google.inject.multibindings explicitly because it is a fragment bundle. 
Starting bundle com.google.inject 
Starting bundle org.fusesource.jansi 
Starting bundle jul.to.slf4j 
Starting bundle log4j.over.slf4j 
Starting bundle ch.qos.logback.classic 
Starting bundle ch.qos.logback.core 
Starting bundle org.apache.servicemix.bundles.aopalliance 
Starting bundle org.apache.servicemix.bundles.javax-inject 
Starting bundle org.eclipse.equinox.common 
Starting bundle org.eclipse.equinox.registry 
Starting bundle org.eclipse.equinox.supplement 
Starting bundle org.semanticweb.owl.owlapi 
Starting bundle org.protege.common 
Starting bundle org.protege.editor.core.application 
Starting bundle org.protege.editor.owl 
Starting bundle slf4j.api 
17:11:06,589 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [conf/logback.xml] at [file:/C:/repositories/protege/protege-desktop/target/protege-5.0.0-beta-23-SNAPSHOT-platform-independent/Protege-5.0.0-beta-23-SNAPSHOT/conf/logback.xml]
17:11:06,613 |-INFO in ch.qos.logback.classic.joran.action.ConfigurationAction - debug attribute not set
17:11:06,616 |-INFO in ch.qos.logback.classic.joran.action.ConfigurationAction - Setting ReconfigureOnChangeFilter scanning period to 10 seconds
17:11:06,616 |-INFO in ReconfigureOnChangeFilter{invocationCounter=0} - Will scan for changes in [[C:\repositories\protege\protege-desktop\target\protege-5.0.0-beta-23-SNAPSHOT-platform-independent\Protege-5.0.0-beta-23-SNAPSHOT\conf\logback.xml]] every 10 seconds. 
17:11:06,616 |-INFO in ch.qos.logback.classic.joran.action.ConfigurationAction - Adding ReconfigureOnChangeFilter as a turbo filter
17:11:06,618 |-INFO in ch.qos.logback.core.joran.action.AppenderAction - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
17:11:06,619 |-INFO in ch.qos.logback.core.joran.action.AppenderAction - Naming appender as [stdout]
17:11:06,654 |-INFO in ch.qos.logback.core.ConsoleAppender[stdout] - Enabling JANSI WindowsAnsiOutputStream for the console.
17:11:06,654 |-WARN in ch.qos.logback.core.ConsoleAppender[stdout] - Failed to create WindowsAnsiOutputStream. Falling back on the default stream. ch.qos.logback.core.util.DynamicClassLoadingException: Failed to instantiate type org.fusesource.jansi.WindowsAnsiOutputStream
    at ch.qos.logback.core.util.DynamicClassLoadingException: Failed to instantiate type org.fusesource.jansi.WindowsAnsiOutputStream
    at  at ch.qos.logback.core.util.OptionHelper.instantiateByClassNameAndParameter(OptionHelper.java:73)
    at  at ch.qos.logback.core.util.OptionHelper.instantiateByClassNameAndParameter(OptionHelper.java:42)
    at  at ch.qos.logback.core.ConsoleAppender.getTargetStreamForWindows(ConsoleAppender.java:94)
    at  at ch.qos.logback.core.ConsoleAppender.start(ConsoleAppender.java:85)
    at  at ch.qos.logback.core.joran.action.AppenderAction.end(AppenderAction.java:96)
    at  at ch.qos.logback.core.joran.spi.Interpreter.callEndAction(Interpreter.java:317)
    at  at ch.qos.logback.core.joran.spi.Interpreter.endElement(Interpreter.java:196)
    at  at ch.qos.logback.core.joran.spi.Interpreter.endElement(Interpreter.java:182)
    at  at ch.qos.logback.core.joran.spi.EventPlayer.play(EventPlayer.java:62)
    at  at ch.qos.logback.core.joran.GenericConfigurator.doConfigure(GenericConfigurator.java:149)
    at  at ch.qos.logback.core.joran.GenericConfigurator.doConfigure(GenericConfigurator.java:135)
    at  at ch.qos.logback.core.joran.GenericConfigurator.doConfigure(GenericConfigurator.java:99)
    at  at ch.qos.logback.core.joran.GenericConfigurator.doConfigure(GenericConfigurator.java:49)
    at  at ch.qos.logback.classic.util.ContextInitializer.configureByResource(ContextInitializer.java:77)
    at  at ch.qos.logback.classic.util.ContextInitializer.autoConfig(ContextInitializer.java:152)
    at  at org.slf4j.impl.StaticLoggerBinder.init(StaticLoggerBinder.java:85)
    at  at org.slf4j.impl.StaticLoggerBinder.<clinit>(StaticLoggerBinder.java:55)
    at  at org.slf4j.LoggerFactory.bind(LoggerFactory.java:141)
    at  at org.slf4j.LoggerFactory.performInitialization(LoggerFactory.java:120)
    at  at org.slf4j.LoggerFactory.getILoggerFactory(LoggerFactory.java:331)
    at  at org.slf4j.LoggerFactory.getLogger(LoggerFactory.java:283)
    at  at org.slf4j.LoggerFactory.getLogger(LoggerFactory.java:304)
    at  at org.protege.common.Activator.<init>(Activator.java:10)
    at  at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
    at  at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source)
    at  at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Source)
    at  at java.lang.reflect.Constructor.newInstance(Unknown Source)
    at  at java.lang.Class.newInstance(Unknown Source)
    at  at org.apache.felix.framework.Felix.createBundleActivator(Felix.java:4362)
    at  at org.apache.felix.framework.Felix.activateBundle(Felix.java:2149)
    at  at org.apache.felix.framework.Felix.startBundle(Felix.java:2072)
    at  at org.apache.felix.framework.Felix.setActiveStartLevel(Felix.java:1299)
    at  at org.apache.felix.framework.FrameworkStartLevelImpl.run(FrameworkStartLevelImpl.java:304)
    at  at java.lang.Thread.run(Unknown Source)
Caused by: java.lang.ClassNotFoundException: org.fusesource.jansi.WindowsAnsiOutputStream not found by ch.qos.logback.classic [14]
    at  at org.apache.felix.framework.BundleWiringImpl.findClassOrResourceByDelegation(BundleWiringImpl.java:1556)
    at  at org.apache.felix.framework.BundleWiringImpl.access$400(BundleWiringImpl.java:77)
    at  at org.apache.felix.framework.BundleWiringImpl$BundleClassLoader.loadClass(BundleWiringImpl.java:1993)
    at  at java.lang.ClassLoader.loadClass(Unknown Source)
    at  at ch.qos.logback.core.util.OptionHelper.instantiateByClassNameAndParameter(OptionHelper.java:60)
    at  ... 33 common frames omitted
17:11:06,655 |-INFO in ch.qos.logback.core.joran.action.AppenderAction - About to instantiate appender of type [ch.qos.logback.core.FileAppender]
17:11:06,655 |-INFO in ch.qos.logback.core.joran.action.AppenderAction - Naming appender as [files]
17:11:06,660 |-INFO in ch.qos.logback.core.FileAppender[files] - File property is set to [C:\Users\user123/.protege/logs/protege.log]
17:11:06,661 |-INFO in ch.qos.logback.classic.joran.action.RootLoggerAction - Setting level of ROOT logger to INFO
17:11:06,661 |-INFO in ch.qos.logback.core.joran.action.AppenderRefAction - Attaching appender named [stdout] to Logger[ROOT]
17:11:06,662 |-INFO in ch.qos.logback.core.joran.action.AppenderRefAction - Attaching appender named [files] to Logger[ROOT]
17:11:06,662 |-INFO in ch.qos.logback.classic.joran.action.ConfigurationAction - End of configuration.
17:11:06,662 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@4d16667c - Registering current configuration as safe fallback point

The OSGi framework has been started 
 
------------------------------------ Protégé ----------------------------------- 
Protégé Desktop 
Version 5.0.0, Build beta-23-SNAPSHOT 
 
 
----------------------------------- Platform ----------------------------------- 
Java: JVM 1.8.0_73-b02  Memory: 466M 
Language: de, Country: DE 
Framework: Apache Software Foundation (1.7)  
OS: windows7 (6.1) 
Processor: x86-64
 
 
------------------------------------ Plugins ----------------------------------- 
No plugins installed 
 
.\run.bat : févr. 17, 2016 5:11:07 PM java.util.prefs.WindowsPreferences <init>
In Zeile:1 Zeichen:1
+ .\run.bat 2>&1 1> "c:\user123\protégé.log"
+ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    + CategoryInfo          : NotSpecified: (févr. 17, 2016 ...ferences <init>:String) [], RemoteException
    + FullyQualifiedErrorId : NativeCommandError

WARNING: Could not open/create prefs root node Software\JavaSoft\Prefs at root 0x80000002. Windows RegCreateKeyEx(...) returned error code 5.

OWL API Version: 4.1.3.20151118-2017 
Cannot generate ontology catalog for ontology at http://www.semanticweb.org/user123/ontologies/2016/1/untitled-ontology-9 
------------------------------- Auto-update Check ------------------------------ 
Auto-update last performed: Wed Feb 17 12:29:12 CET 2016 
Auto-update has been performed today.  Not performing it again. 
 
### Excluding compile: javax.swing.text.GlyphView::getBreakSpot
OWL API Version: 4.1.3.20151118-2017 
------------------------------- Loading Ontology ------------------------------- 
Loading ontology from file:/C:/FILES/user123/+thesis/voc/mathematics/lattice%20theory.ttl 
Folder repository probably came from another system 
Could not be updated because directory C:\user123\P71 Thèse\ontologies does not exist 
Bad ontology library declaration - check logs. Warnings now disabled for this session. 
java.io.IOException: null
    at org.protege.editor.owl.model.library.folder.FolderGroupManager.isSuitable(FolderGroupManager.java:96) [protege-editor-owl.jar:na]
    at org.protege.editor.owl.model.library.OntologyCatalogManager.update(OntologyCatalogManager.java:157) [protege-editor-owl.jar:na]
    at org.protege.editor.owl.model.library.OntologyCatalogManager.ensureCatalogExists(OntologyCatalogManager.java:115) [protege-editor-owl.jar:na]
    at org.protege.editor.owl.model.library.OntologyCatalogManager.addFolder(OntologyCatalogManager.java:188) [protege-editor-owl.jar:na]
    at org.protege.editor.owl.model.OWLModelManagerImpl.addRootFolder(OWLModelManagerImpl.java:319) [protege-editor-owl.jar:na]
    at org.protege.editor.owl.model.OWLModelManagerImpl.loadOntologyFromPhysicalURI(OWLModelManagerImpl.java:274) [protege-editor-owl.jar:na]
    at org.protege.editor.owl.OWLEditorKit.handleLoadFrom(OWLEditorKit.java:201) [protege-editor-owl.jar:na]
    at org.protege.editor.owl.OWLEditorKit.handleLoadRecentRequest(OWLEditorKit.java:189) [protege-editor-owl.jar:na]
    at org.protege.editor.core.ProtegeManager.openAndSetupRecentEditorKit(ProtegeManager.java:263) [protege-editor-core.jar:na]
    at org.protege.editor.core.ui.action.OpenRecentAction$RecentEditorKitAction.openInNewWorkspace(OpenRecentAction.java:90) [protege-editor-core.jar:na]
    at org.protege.editor.core.ui.util.UIUtil.openRequest(UIUtil.java:210) [protege-editor-core.jar:na]
    at org.protege.editor.core.ui.action.OpenRecentAction$RecentEditorKitAction.actionPerformed(OpenRecentAction.java:76) [protege-editor-core.jar:na]
    at javax.swing.AbstractButton.fireActionPerformed(Unknown Source) [na:1.8.0_73]
    at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source) [na:1.8.0_73]
    at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source) [na:1.8.0_73]
    at javax.swing.DefaultButtonModel.setPressed(Unknown Source) [na:1.8.0_73]
    at javax.swing.AbstractButton.doClick(Unknown Source) [na:1.8.0_73]
    at javax.swing.plaf.basic.BasicMenuItemUI.doClick(Unknown Source) [na:1.8.0_73]
    at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(Unknown Source) [na:1.8.0_73]
    at java.awt.Component.processMouseEvent(Unknown Source) [na:1.8.0_73]
    at javax.swing.JComponent.processMouseEvent(Unknown Source) [na:1.8.0_73]
    at java.awt.Component.processEvent(Unknown Source) [na:1.8.0_73]
    at java.awt.Container.processEvent(Unknown Source) [na:1.8.0_73]
    at java.awt.Component.dispatchEventImpl(Unknown Source) [na:1.8.0_73]
    at java.awt.Container.dispatchEventImpl(Unknown Source) [na:1.8.0_73]
    at java.awt.Component.dispatchEvent(Unknown Source) [na:1.8.0_73]
    at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source) [na:1.8.0_73]
    at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source) [na:1.8.0_73]
    at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source) [na:1.8.0_73]
    at java.awt.Container.dispatchEventImpl(Unknown Source) [na:1.8.0_73]
    at java.awt.Window.dispatchEventImpl(Unknown Source) [na:1.8.0_73]
    at java.awt.Component.dispatchEvent(Unknown Source) [na:1.8.0_73]
    at java.awt.EventQueue.dispatchEventImpl(Unknown Source) [na:1.8.0_73]
    at java.awt.EventQueue.access$500(Unknown Source) [na:1.8.0_73]
    at java.awt.EventQueue$3.run(Unknown Source) [na:1.8.0_73]
    at java.awt.EventQueue$3.run(Unknown Source) [na:1.8.0_73]
    at java.security.AccessController.doPrivileged(Native Method) [na:1.8.0_73]
    at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) [na:1.8.0_73]
    at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) [na:1.8.0_73]
    at java.awt.EventQueue$4.run(Unknown Source) [na:1.8.0_73]
    at java.awt.EventQueue$4.run(Unknown Source) [na:1.8.0_73]
    at java.security.AccessController.doPrivileged(Native Method) [na:1.8.0_73]
    at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) [na:1.8.0_73]
    at java.awt.EventQueue.dispatchEvent(Unknown Source) [na:1.8.0_73]
    at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source) [na:1.8.0_73]
    at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source) [na:1.8.0_73]
    at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source) [na:1.8.0_73]
    at java.awt.EventDispatchThread.pumpEvents(Unknown Source) [na:1.8.0_73]
    at java.awt.EventDispatchThread.pumpEvents(Unknown Source) [na:1.8.0_73]
    at java.awt.EventDispatchThread.run(Unknown Source) [na:1.8.0_73]
LOGBACK: No context given for org.protege.editor.core.log.LogManager$1[null]
Folder repository probably came from another system 
Could not be updated because directory C:\user123\P71 thesis\voc does not exist 
Loading OntologyID(Anonymous-0) from file:/C:/FILES/user123/+thesis/voc/mathematics/lattice%20theory.ttl 
dumping remaining triples 
done dumping remaining triples 
Loading for ontology and imports closure successfully completed in 198 ms 
 
---------------------------- Disposing of Workspace ---------------------------- 
Saved tab state for 'Active Ontology' tab 
Saved tab state for 'Individuals by class' tab 
Saved tab state for 'Entities' tab 
Saved tab state for 'Annotation Properties' tab 
Saved tab state for 'Data Properties' tab 
Saved tab state for 'Object Properties' tab 
Saved tab state for 'Classes' tab 
Saved workspace 
Disposed of 'Active Ontology' tab 
Disposed of 'Individuals by class' tab 
Disposed of 'Entities' tab 
Disposed of 'Annotation Properties' tab 
Disposed of 'Data Properties' tab 
Disposed of 'Object Properties' tab 
Disposed of 'Classes' tab 
Disposed of workspace 
 
---------------------------- Disposing of Workspace ---------------------------- 
Saved tab state for 'Active Ontology' tab 
Saved tab state for 'Object Properties' tab 
Saved tab state for 'Individuals by class' tab 
Saved tab state for 'Data Properties' tab 
Saved tab state for 'Annotation Properties' tab 
Saved tab state for 'Classes' tab 
Saved tab state for 'Entities' tab 
Saved workspace 
Disposed of 'Active Ontology' tab 
Disposed of 'Object Properties' tab 
Disposed of 'Individuals by class' tab 
Disposed of 'Data Properties' tab 
Disposed of 'Annotation Properties' tab 
Disposed of 'Classes' tab 
Disposed of 'Entities' tab 
Disposed of workspace 
 

Screenshots:

duplicate prefixes for annotations duplicate prefixes for classess renderer advanced settings renderer settings